scPriorGraph: constructing biosemantic cell–cell graphs with prior gene set selection for cell type identification from scRNA-seq data

Abstract

Abstract Cell type identification is an indispensable analytical step in single-cell data analyses. To address the high noise stemming from gene expression data, existing computational methods often overlook the biologically meaningful relationships between genes, opting to reduce all genes to a unified data space. We assume that such relationships can aid in characterizing cell type features and improving cell type recognition accuracy. To this end, we introduce scPriorGraph, a dual-channel graph neural network that integrates multi-level gene biosemantics. Experimental results demonstrate that scPriorGraph effectively aggregates feature values of similar cells using high-quality graphs, achieving state-of-the-art performance in cell type identification.

Keywords

• Single-cell RNA sequencing
• Cell-type identification
• Dual-channel graph neural network
• Pathway
• Ligand-receptor network
• Graph augmentation